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This page was generated on 2021-12-01 17:18:24 -0500 (Wed, 01 Dec 2021).

CHECK results for microbiomeMarker on machv2

To the developers/maintainers of the microbiomeMarker package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/microbiomeMarker.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1144/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiomeMarker 1.0.1  (landing page)
Yang Cao
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/microbiomeMarker
git_branch: RELEASE_3_14
git_last_commit: d4852b9
git_last_commit_date: 2021-11-08 03:46:16 -0500 (Mon, 08 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: microbiomeMarker
Version: 1.0.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:microbiomeMarker.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings microbiomeMarker_1.0.1.tar.gz
StartedAt: 2021-11-30 18:36:20 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 18:46:45 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 624.9 seconds
RetCode: 0
Status:   OK  
CheckDir: microbiomeMarker.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:microbiomeMarker.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings microbiomeMarker_1.0.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/microbiomeMarker.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microbiomeMarker/DESCRIPTION’ ... OK
* this is package ‘microbiomeMarker’ version ‘1.0.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘microbiomeMarker’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
run_deseq2               16.182  0.039  16.259
run_ancombc              14.061  0.044  14.124
plot_cladogram           11.960  0.156  12.125
run_aldex                10.748  0.670  11.483
plot_heatmap              9.945  0.082  10.037
plot_sl_roc               9.297  0.105   9.419
run_lefse                 8.221  0.048   8.298
plot_abundance            6.724  0.019   6.757
run_metagenomeseq         5.803  0.033   5.840
run_edger                 5.788  0.021   5.816
run_test_multiple_groups  5.168  0.012   5.186
effect_size-plot          4.934  0.034   5.038
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

microbiomeMarker.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL microbiomeMarker
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘microbiomeMarker’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (microbiomeMarker)

Tests output

microbiomeMarker.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(microbiomeMarker)
> 
> test_check("microbiomeMarker")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 11 | SKIP 1 | PASS 194 ]
> 
> proc.time()
   user  system elapsed 
100.183   2.206 102.552 

Example timings

microbiomeMarker.Rcheck/microbiomeMarker-Ex.timings

nameusersystemelapsed
abundances-methods0.2360.0110.247
aggregate_taxa1.3570.0111.368
assign-marker_table4.6410.1424.923
effect_size-plot4.9340.0345.038
extract_posthoc_res0.1590.0060.166
import_dada20.0790.0020.083
import_qiime20.2990.0510.359
marker_table-methods4.5940.0114.648
microbiomeMarker0.0260.0020.028
nmarker-methods0.0030.0010.003
normalize-methods0.1700.0090.200
phyloseq2DESeq21.1690.0091.191
phyloseq2edgeR0.1770.0090.186
phyloseq2metagenomeSeq0.2970.0060.304
plot_abundance6.7240.0196.757
plot_cladogram11.960 0.15612.125
plot_heatmap 9.945 0.08210.037
plot_postHocTest1.5970.0071.605
plot_sl_roc9.2970.1059.419
postHocTest0.1440.0060.151
run_aldex10.748 0.67011.483
run_ancom0.0000.0000.001
run_ancombc14.061 0.04414.124
run_deseq216.182 0.03916.259
run_edger5.7880.0215.816
run_lefse8.2210.0488.298
run_limma_voom4.6710.0114.684
run_metagenomeseq5.8030.0335.840
run_posthoc_test0.8980.0090.908
run_simple_stat4.4110.0174.522
run_sl3.6350.0193.657
run_test_multiple_groups5.1680.0125.186
run_test_two_groups4.5540.0134.570
subset_marker4.4660.0134.484
summarize_taxa0.6690.0040.673
transform_abundances0.2250.0460.270